Multiple sequence alignment - TraesCS1D01G178700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G178700 chr1D 100.000 2694 0 0 1 2694 254381804 254379111 0.000000e+00 4939.0
1 TraesCS1D01G178700 chr1D 97.164 2010 35 2 1 2009 298350413 298348425 0.000000e+00 3376.0
2 TraesCS1D01G178700 chr1D 96.967 2011 37 3 1 2009 254525823 254527811 0.000000e+00 3354.0
3 TraesCS1D01G178700 chr1D 81.844 705 100 14 2007 2694 209086940 209086247 3.890000e-158 568.0
4 TraesCS1D01G178700 chr1D 80.672 714 98 13 2007 2693 164547540 164548240 3.980000e-143 518.0
5 TraesCS1D01G178700 chr1D 80.056 712 102 14 2007 2694 253626032 253626727 2.410000e-135 492.0
6 TraesCS1D01G178700 chr1D 78.011 714 116 16 2008 2694 69549306 69550005 6.940000e-111 411.0
7 TraesCS1D01G178700 chr3A 97.760 2009 24 1 1 2009 66004915 66002928 0.000000e+00 3441.0
8 TraesCS1D01G178700 chr3A 88.525 61 7 0 2609 2669 340436372 340436312 1.030000e-09 75.0
9 TraesCS1D01G178700 chr6D 97.710 2009 25 1 1 2009 389245604 389243617 0.000000e+00 3435.0
10 TraesCS1D01G178700 chr6D 79.858 422 81 4 2174 2593 341862809 341862390 3.370000e-79 305.0
11 TraesCS1D01G178700 chr6D 89.447 199 0 1 1 199 145354985 145354808 5.800000e-57 231.0
12 TraesCS1D01G178700 chr6D 76.699 309 57 15 2009 2307 280531213 280530910 9.980000e-35 158.0
13 TraesCS1D01G178700 chr5D 97.611 2009 27 1 1 2009 503264558 503262571 0.000000e+00 3424.0
14 TraesCS1D01G178700 chr5D 97.511 2009 29 1 1 2009 503245490 503247477 0.000000e+00 3413.0
15 TraesCS1D01G178700 chr5D 96.223 1562 30 5 1 1560 432435473 432437007 0.000000e+00 2531.0
16 TraesCS1D01G178700 chr5D 95.233 881 17 3 1 877 329136370 329135511 0.000000e+00 1371.0
17 TraesCS1D01G178700 chr5D 78.711 714 108 21 2007 2694 215823153 215823848 1.150000e-118 436.0
18 TraesCS1D01G178700 chr3D 97.511 2009 29 3 1 2009 589263308 589261321 0.000000e+00 3415.0
19 TraesCS1D01G178700 chr3D 79.853 680 104 10 2007 2663 314882177 314881508 1.460000e-127 466.0
20 TraesCS1D01G178700 chr3D 77.857 700 106 23 2026 2694 283632364 283633045 3.250000e-104 388.0
21 TraesCS1D01G178700 chr2A 97.511 2009 29 1 1 2009 726906237 726904250 0.000000e+00 3413.0
22 TraesCS1D01G178700 chr2D 97.461 2009 30 1 1 2009 591984827 591986814 0.000000e+00 3408.0
23 TraesCS1D01G178700 chr2D 98.487 1917 29 0 93 2009 272811957 272810041 0.000000e+00 3380.0
24 TraesCS1D01G178700 chr2D 78.134 718 115 20 2008 2694 276851322 276850616 4.150000e-113 418.0
25 TraesCS1D01G178700 chr2D 83.425 181 26 4 2007 2184 425968552 425968373 5.970000e-37 165.0
26 TraesCS1D01G178700 chr2D 82.967 182 30 1 2007 2187 222792604 222792423 2.150000e-36 163.0
27 TraesCS1D01G178700 chr7B 97.262 2009 34 1 1 2009 663099207 663097220 0.000000e+00 3386.0
28 TraesCS1D01G178700 chr7B 79.774 707 110 16 2007 2694 421025423 421024731 1.450000e-132 483.0
29 TraesCS1D01G178700 chr5B 80.028 706 109 20 2008 2694 204261777 204262469 6.700000e-136 494.0
30 TraesCS1D01G178700 chr1B 78.182 715 117 19 2007 2694 492209660 492210362 1.150000e-113 420.0
31 TraesCS1D01G178700 chr3B 77.684 708 108 19 2007 2682 654012696 654012007 1.170000e-103 387.0
32 TraesCS1D01G178700 chr3B 78.446 399 55 11 2008 2379 491287398 491287004 5.800000e-57 231.0
33 TraesCS1D01G178700 chr3B 81.250 272 29 7 2007 2257 382959898 382959628 1.640000e-47 200.0
34 TraesCS1D01G178700 chr7D 77.966 649 93 25 2008 2632 324917874 324918496 7.090000e-96 361.0
35 TraesCS1D01G178700 chr4A 76.364 715 120 20 2007 2692 346689440 346690134 3.320000e-89 339.0
36 TraesCS1D01G178700 chr4A 84.783 184 25 3 2007 2188 222898104 222897922 5.920000e-42 182.0
37 TraesCS1D01G178700 chr4A 85.227 88 7 3 2609 2693 229392642 229392558 4.780000e-13 86.1
38 TraesCS1D01G178700 chr2B 75.410 671 127 18 2049 2694 297797448 297798105 9.440000e-75 291.0
39 TraesCS1D01G178700 chr2B 83.333 180 28 2 2007 2185 337921312 337921134 5.970000e-37 165.0
40 TraesCS1D01G178700 chr1A 90.749 227 0 1 1 227 549269900 549270105 1.580000e-72 283.0
41 TraesCS1D01G178700 chrUn 89.655 203 0 1 1 203 470004642 470004823 3.470000e-59 239.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G178700 chr1D 254379111 254381804 2693 True 4939 4939 100.000 1 2694 1 chr1D.!!$R2 2693
1 TraesCS1D01G178700 chr1D 298348425 298350413 1988 True 3376 3376 97.164 1 2009 1 chr1D.!!$R3 2008
2 TraesCS1D01G178700 chr1D 254525823 254527811 1988 False 3354 3354 96.967 1 2009 1 chr1D.!!$F4 2008
3 TraesCS1D01G178700 chr1D 209086247 209086940 693 True 568 568 81.844 2007 2694 1 chr1D.!!$R1 687
4 TraesCS1D01G178700 chr1D 164547540 164548240 700 False 518 518 80.672 2007 2693 1 chr1D.!!$F2 686
5 TraesCS1D01G178700 chr1D 253626032 253626727 695 False 492 492 80.056 2007 2694 1 chr1D.!!$F3 687
6 TraesCS1D01G178700 chr1D 69549306 69550005 699 False 411 411 78.011 2008 2694 1 chr1D.!!$F1 686
7 TraesCS1D01G178700 chr3A 66002928 66004915 1987 True 3441 3441 97.760 1 2009 1 chr3A.!!$R1 2008
8 TraesCS1D01G178700 chr6D 389243617 389245604 1987 True 3435 3435 97.710 1 2009 1 chr6D.!!$R4 2008
9 TraesCS1D01G178700 chr5D 503262571 503264558 1987 True 3424 3424 97.611 1 2009 1 chr5D.!!$R2 2008
10 TraesCS1D01G178700 chr5D 503245490 503247477 1987 False 3413 3413 97.511 1 2009 1 chr5D.!!$F3 2008
11 TraesCS1D01G178700 chr5D 432435473 432437007 1534 False 2531 2531 96.223 1 1560 1 chr5D.!!$F2 1559
12 TraesCS1D01G178700 chr5D 329135511 329136370 859 True 1371 1371 95.233 1 877 1 chr5D.!!$R1 876
13 TraesCS1D01G178700 chr5D 215823153 215823848 695 False 436 436 78.711 2007 2694 1 chr5D.!!$F1 687
14 TraesCS1D01G178700 chr3D 589261321 589263308 1987 True 3415 3415 97.511 1 2009 1 chr3D.!!$R2 2008
15 TraesCS1D01G178700 chr3D 314881508 314882177 669 True 466 466 79.853 2007 2663 1 chr3D.!!$R1 656
16 TraesCS1D01G178700 chr3D 283632364 283633045 681 False 388 388 77.857 2026 2694 1 chr3D.!!$F1 668
17 TraesCS1D01G178700 chr2A 726904250 726906237 1987 True 3413 3413 97.511 1 2009 1 chr2A.!!$R1 2008
18 TraesCS1D01G178700 chr2D 591984827 591986814 1987 False 3408 3408 97.461 1 2009 1 chr2D.!!$F1 2008
19 TraesCS1D01G178700 chr2D 272810041 272811957 1916 True 3380 3380 98.487 93 2009 1 chr2D.!!$R2 1916
20 TraesCS1D01G178700 chr2D 276850616 276851322 706 True 418 418 78.134 2008 2694 1 chr2D.!!$R3 686
21 TraesCS1D01G178700 chr7B 663097220 663099207 1987 True 3386 3386 97.262 1 2009 1 chr7B.!!$R2 2008
22 TraesCS1D01G178700 chr7B 421024731 421025423 692 True 483 483 79.774 2007 2694 1 chr7B.!!$R1 687
23 TraesCS1D01G178700 chr5B 204261777 204262469 692 False 494 494 80.028 2008 2694 1 chr5B.!!$F1 686
24 TraesCS1D01G178700 chr1B 492209660 492210362 702 False 420 420 78.182 2007 2694 1 chr1B.!!$F1 687
25 TraesCS1D01G178700 chr3B 654012007 654012696 689 True 387 387 77.684 2007 2682 1 chr3B.!!$R3 675
26 TraesCS1D01G178700 chr7D 324917874 324918496 622 False 361 361 77.966 2008 2632 1 chr7D.!!$F1 624
27 TraesCS1D01G178700 chr4A 346689440 346690134 694 False 339 339 76.364 2007 2692 1 chr4A.!!$F1 685
28 TraesCS1D01G178700 chr2B 297797448 297798105 657 False 291 291 75.410 2049 2694 1 chr2B.!!$F1 645

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
599 607 0.824759 ACTACGAGATCACCCCAAGC 59.175 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2083 0.534652 GGCCTTTTTGCATGCACCAA 60.535 50.0 22.58 13.76 0.0 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 2.985282 CAGCTGCGCCAGGGAAAA 60.985 61.111 4.18 0.00 31.21 2.29
599 607 0.824759 ACTACGAGATCACCCCAAGC 59.175 55.000 0.00 0.00 0.00 4.01
696 704 1.765074 GGTTGGGCAGTAAGGGTCA 59.235 57.895 0.00 0.00 0.00 4.02
781 789 3.378399 GAGAGCTCCCCGTTCCTGC 62.378 68.421 10.93 0.00 0.00 4.85
810 818 1.859841 AACTGGATTCCCCGGAACCC 61.860 60.000 0.73 0.00 44.44 4.11
1028 1036 1.677052 GGTTCGAGTCCGCTTATCTCT 59.323 52.381 0.00 0.00 35.37 3.10
1304 1312 2.548067 CCGGAGATTCCCAAATAGGTCG 60.548 54.545 0.00 0.00 31.13 4.79
1335 1343 0.913924 TGCCTGCTGAATCCATGAGA 59.086 50.000 0.00 0.00 0.00 3.27
1376 1384 4.865365 GCGAACTGAAACATCTTAGTAGCT 59.135 41.667 0.00 0.00 0.00 3.32
1430 1438 2.125106 GGCGAGCGAAATGGGAGT 60.125 61.111 0.00 0.00 0.00 3.85
1471 1479 2.357154 GGGTTGTGGGAGAGCAATACAT 60.357 50.000 0.00 0.00 0.00 2.29
1681 1689 2.673258 GGAAAGGTGAAAAGAACCCCA 58.327 47.619 0.00 0.00 38.57 4.96
1772 1780 1.075542 CGCGTGCCTGTTGAAGAATA 58.924 50.000 0.00 0.00 0.00 1.75
1795 1803 1.517832 GGCGACTCATAGGCAGTGT 59.482 57.895 0.00 0.00 0.00 3.55
1893 1901 1.000163 CCGAACCTGGGTGATCTATCG 60.000 57.143 0.00 0.00 0.00 2.92
1899 1907 3.161067 CCTGGGTGATCTATCGATGACT 58.839 50.000 8.54 0.00 34.64 3.41
1934 1942 3.055094 GGATGAAACTAAGCAGAGGTCCA 60.055 47.826 0.00 0.00 0.00 4.02
2073 2083 1.005630 GCTCGACCTGACAACTGCT 60.006 57.895 0.00 0.00 0.00 4.24
2127 2138 3.766691 GAGTGGCCGGCGGTTAGA 61.767 66.667 28.82 5.99 0.00 2.10
2371 2439 4.658786 ACCCCCTCGAAGGCTGGT 62.659 66.667 0.00 0.00 35.10 4.00
2405 2473 4.410400 GTGGGGGTGCTCCTTCCG 62.410 72.222 4.53 0.00 35.33 4.30
2444 2513 4.437587 GGGGCAGCCACAGCAGAT 62.438 66.667 15.19 0.00 43.56 2.90
2514 2583 1.618640 GCTGACGCGTCTTTGGAGTC 61.619 60.000 36.27 18.05 0.00 3.36
2659 2732 3.326385 TAGGGCCTCGTGGGTGGAT 62.326 63.158 10.74 0.00 37.43 3.41
2673 2746 1.178276 GTGGATGTCGAGGTCACTCT 58.822 55.000 0.00 0.00 41.71 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
418 425 2.042435 AAGCCTAGGAGAGCCGCT 60.042 61.111 14.75 0.00 39.96 5.52
696 704 1.270907 ACGAGTGATTGCCCTTCTCT 58.729 50.000 0.00 0.00 0.00 3.10
781 789 3.118223 GGGGAATCCAGTTACAGGAGAAG 60.118 52.174 0.09 0.00 38.83 2.85
1028 1036 0.966875 TCCGCTAAGTTCACGGGCTA 60.967 55.000 14.52 0.00 46.87 3.93
1248 1256 1.073125 TCAACTCCCCGAAGCATTTCA 59.927 47.619 0.00 0.00 32.67 2.69
1304 1312 2.884639 TCAGCAGGCAGTTTAAAAGGTC 59.115 45.455 0.00 0.00 0.00 3.85
1335 1343 0.538287 GCCAGGTTGTCTCTTGCCTT 60.538 55.000 0.00 0.00 0.00 4.35
1376 1384 4.819630 TCGCTTTTGCTTTCTTTTCCTCTA 59.180 37.500 0.00 0.00 44.80 2.43
1471 1479 3.049674 GCCTAGCAGCACAACGCA 61.050 61.111 0.00 0.00 46.13 5.24
1681 1689 5.011329 TCACGTTCTATTTCACTACCCACTT 59.989 40.000 0.00 0.00 0.00 3.16
1772 1780 2.815308 CCTATGAGTCGCCGGCTT 59.185 61.111 26.68 10.06 0.00 4.35
1795 1803 2.224597 GGTTCCGTTCCCTTAACCAAGA 60.225 50.000 0.00 0.00 40.89 3.02
1826 1834 3.564235 TTAAGACTCGCTTTCGCTACA 57.436 42.857 0.00 0.00 38.05 2.74
1893 1901 4.679373 TCCAAGCTTCATCCTAGTCATC 57.321 45.455 0.00 0.00 0.00 2.92
1899 1907 5.441718 AGTTTCATCCAAGCTTCATCCTA 57.558 39.130 0.00 0.00 0.00 2.94
1934 1942 5.063204 TGATTCTTCAACATCAGTCGGTTT 58.937 37.500 0.00 0.00 0.00 3.27
2073 2083 0.534652 GGCCTTTTTGCATGCACCAA 60.535 50.000 22.58 13.76 0.00 3.67
2113 2124 3.305177 GAAGTCTAACCGCCGGCCA 62.305 63.158 23.46 2.28 0.00 5.36
2127 2138 6.444704 TCTCCCATTTATAGTCAGAGGAAGT 58.555 40.000 0.00 0.00 0.00 3.01
2442 2511 2.435938 TCGCGTGCTTTCCCCATC 60.436 61.111 5.77 0.00 0.00 3.51
2444 2513 3.758973 TTGTCGCGTGCTTTCCCCA 62.759 57.895 5.77 0.00 0.00 4.96
2450 2519 2.877974 GAACGGTTGTCGCGTGCTT 61.878 57.895 5.77 0.00 43.89 3.91
2451 2520 3.335534 GAACGGTTGTCGCGTGCT 61.336 61.111 5.77 0.00 43.89 4.40
2535 2604 2.099652 CTGGAACCAGACACCTGCGA 62.100 60.000 14.94 0.00 46.30 5.10
2673 2746 3.053291 GGAACACATTGCCGGCGA 61.053 61.111 21.20 21.20 0.00 5.54


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.